Investigating the dynamics of Salmonella contamination in integrated poultry companies using a whole genome sequencing approach

Abstract

The study of non-typhoid Salmonella in broiler integrations has been limited by the resolution of typing techniques. Although serotyping of Salmonella isolates is used as a traditional approach, it is not of enough resolution to clearly understand the dynamics of this pathogen within poultry companies. The aim of this research was to investigate the epidemiology and population dynamics of Salmonella serotypes in 2 poultry integrations using a whole genome sequencing approach. Two hundred and forty-three Salmonella isolates recovered from the broiler production chain of 2 integrated poultry companies were whole genome sequenced and analyzed with dedicated databases and bioinformatic software. The analyses of sequences revealed that S . Infantis was the most frequent serotype (82.3%). Most isolates showed a potential for resistance against medically important antibiotics and disinfectants. Furthermore, 97.5% of isolates harbored the pESI-like mega plasmid, that plays an important role in the global dissemination of AMR. SNP tree analysis showed that there were clones that are niche-specific while other ones were distributed throughout the broiler production chains. In this study, we demonstrated the potential of whole genome sequencing analysis for a comprehensive understanding of Salmonella distribution in integrated poultry companies. Data obtained with these techniques allow determination of the presence of genetic factors that play an important role in the environmental fitness and pathogenicity of Salmonella .

Persistence of microbiological hazards in food and feed production and processing environments

“…The AMR in strains of serovars Rissen and Infantis from studies in pork and poultry, respectively, was shown to be plasmid‐mediated (Medina‐Santana et al., 2022; Prasertsee et al., 2019). A proportion of 97.5% of S .…”

“…The AMR in strains of serovars Rissen and Infantis from studies in pork and poultry, respectively, was shown to be plasmid-mediated (Medina-Santana et al, 2022;Prasertsee et al, 2019). A proportion of 97.5% of S. Infantis isolates from the meat sector harboured the pESI-like mega plasmid that plays an important role in global AMR dissemination (Medina-Santana et al, 2022;Vinueza-Burgos et al, 2019).…”

“…The numbers indicate the cases of persistence being identified from the experimental studies retrieved in the literature search for each serotype and sector. Note : Based on (Arguello, Carvajal, et al., 2013; Bersot et al., 2021; Bertrand et al., 2010; Boubendir et al., 2021; Bridier et al., 2019; Corcoran et al., 2013; Dantas et al., 2020; Davies et al., 1997; Duggan et al., 2010; Eriksson et al., 2005; Friesema et al., 2014; Gantzhom et al., 2014; Gosling et al., 2022; Grasso et al., 2015; Gu et al., 2020; Häggblom, 2012; Hiko et al., 2016; Hoffmann et al., 2020; Jakociune et al., 2014; Jones et al., 2019; Kawakami et al., 2019; Keaton et al., 2022; Kim et al., 2015; Kinross et al., 2014; Kuhn et al., 2013; Labska et al., 2021; Lienemann et al., 2011; Löfström et al., 2006; Mannion et al., 2012; Medina‐Santana et al., 2022; Moffatt et al., 2017; Monte et al., 2020; Monte et al., 2022; Moretro et al., 2003; Morganti et al., 2018; Morita et al., 2022; Nesse et al., 2003; Nesse et al., 2005; Parker et al., 2019; Parker et al., 2022; Pellegrini et al., 2015; Piras et al., 2011; Piras et al., 2015; Prasertsee et al., 2019; Prendergast et al., 2011; Ren et al., 2016; Russo et al., 2013; Schroeder et al., 2016; Tadee et al., 2015; Trinetta et al., 2020; van Hoek et al., 2012; Viazis et al., 2015; Vinueza‐Burgos et al., 2019; Wang et al., …”

“…A proportion of 97.5% of S . Infantis isolates from the meat sector harboured the pESI‐like mega plasmid that plays an important role in global AMR dissemination (Medina‐Santana et al., 2022; Vinueza‐Burgos et al., 2019).…”

Phenotypic and genotypic characterization of antimicrobial resistance profiles in Salmonella isolated from waterfowl in 2002–2005 and 2018–2020 in Sichuan, China

“…Thus, it is of interest and importance to perform continuous AMR monitoring and to investigate changes in AMR over time, which is crucial in identifying the mechanisms involved and providing guidance on rational treatment strategies. Characterization of Salmonella resistance is mainly performed by determining phenotypes based on antimicrobial susceptibility testing (AST; CLSI, 2020 ) and genotypes based on whole-genome sequencing (WGS; Schwan et al, 2021 ; Yan et al, 2021 ; Medina-Santana et al, 2022 ). Phenotypes usually correspond to the external expression of a single gene but may also be the result of synergistic effects of multiple genes ( Morales et al, 2005 ).…”